mutalyzer.conf

#
# Mutalyzer config file.
#


#
# These settings are used by the Retriever module.
#

# Use this email address for retrieval of records at the NCBI.
email = "mutalyzer@humgen.nl"

# The cache directory.
cache = "./var/cache"

# The maximum size of the cache in megabytes.
cachesize = 50

# The maximum size of a downloaded GenBank file in megabytes.
maxDldSize = 10

# The minimum size of a downloaded GenBank file in bytes.
minDldSize = 512


#
# These settings are used by the Db module.
#

# Internal database.
internalDb = "mutalyzer"

# MySQL mapping database names.
dbNames = "hg18", "hg19"

# MySQL username for the local databases (inernalDb and dnNames).
LocalMySQLuser = "mutalyzer"

# Host name for the local databases.
LocalMySQLhost = "localhost"

# MySQL username for the UCSC database.
RemoteMySQLuser = "genome"

# Host name for the UCSC database.
RemoteMySQLhost = "genome-mysql.cse.ucsc.edu"

# Retrieve all entries modified within a certain number of days.
UpdateInterval = 7

# Temporary file for updated UCSC mapping information.
TempFile = "./var/UCSC_Update.txt"


#
# These settings are used by the Output module.
#

# Name and location of the log file.
log = "./var/mutalyzer.log"

# Prefix for each log message.
datestring = "%Y-%m-%d %H:%M:%S"

# Message levels:
#
# 0 : Debug   ; Show all messages.
# 1 : Info    ; Show all messages except debug messages.
# 2 : Warning ; Show warning, error and fatal messages.
# 3 : Error   ; Show error and fatal messages.
# 4 : Fatal   ; Only show fatal messages.
# 5 : Off     ; Show nothing.

# Level of logged messages.
loglevel = 3

# Level of output messages.
outputlevel = 1


#
# These settings are used by the Mutator module.
#

# Length of the flanking sequences (used in the visualisation of mutations).
flanksize = 25

# Maximum length of visualised mutations.
maxvissize = 25

# Length of the flanking sequences of the clipped mutations (see maxvissize).
flankclipsize = 6


#
# These settings are used by the Scheduler module.
#

# Name of the batch process.
processName = "MutalyzerBatch2"

# Return e-mail address.
mailFrom = "noreply@humgen.nl"

# Location of the mail template.
mailMessage = "./mail.txt"

# Subject of the message.
mailSubject = "Result of Mutalyzer batch check."

# Location of the results.
resultsDir = "./var/cache"

# Location of the PID file.
PIDfile = "./var/batch.pid"

# The output header for NameChecking
nameCheckOutHeader = "Input", "Errors | Messages", "AccNo", "Genesymbol", "Variant", "Reference Sequence Start Descr.", "Coding DNA Descr.", "Protein Descr.", "GeneSymbol Coding DNA Descr.", "GeneSymbol Protein Descr.", "Genomic Reference", "Coding Reference", "Protein Reference", "Affected Transcripts", "Affected Proteins"

# The output header for NameChecking
syntaxCheckOutHeader = "Input", "Status"

# The output header for NameChecking
positionConverterOutHeader = "Input Variant", "Errors", "Chromosomal Variant", "Coding Variant(s)"

#
# These settings are used by the File module.
#

# Amount of bytes to be read for determining the file type.
bufSize = 32768

# The obligatory header in batch request files.
header = "AccNo", "Genesymbol", "Mutation"


# Directory for temporary files.
tempDir = "./var"


#
# These settings are used by the GenRecord module.
#

# Number of upstream nucleotides when searching for a transcript.
upstream = 5000

# Number of downstream nucleotides when searching for a transcript.
downstream = 2000

spliceAlarm = 2

spliceWarn = 5